Just installed a nice car stereo system in my car & iam experiencing engine whine through the speakers more noticable on low volume.

I have fitted Sony head unit, upgraded all speakers & fitted two 10inch subs via two amps.
I have upgraded all the wiring. I made sure the main power to the amps runs opposite side of the car to the rca leads.

Although they probably become close near the amp.
Any ideas???

Where are the amps, if they are in the boot have you used the 10mm lug under the nearside rear lights for an earth as thats the best point in the boot, make sure its nice and clean.
Can you turn off or disconnect the amps to the headunit to see if it is the cabling going to the amps.
If you still have whine after that try moving balance around on speakers to see if they are all the same.
You might have to get some supressors for the incoming power to the headunit.
Had much the same problem but whoever put the amps in my boot put all the wires down the centre of the car. Found most of the noise was from them and the poor earth they used , still have some but have yet to reroute power away from rca leads.

I have routed my cables down the centre too the rca's one side & the Power the other.
Then the speaker cables run down the sides.
I will do the checks that you have suggested & see if i can isolate the problem.

Cheers